add rate subsitution, insertion, deletion in data

src/data_formatting.py

@@ -73,6 +73,8 @@ for file in files_alignement:
 		occurence_similarity = Counter(similarity)
 		nb_ambiguity=0
 		nb_identity=0
+		nb_deletion=0
+		nb_insertion=0
 
 		for i in "RYSWKMBDHVN":
 			if (i in occurence_seq):
@@ -88,6 +90,12 @@ for file in files_alignement:
 		for i in range(0,len(seq)):
 			if(seq[i]==hsp.hit[i]):
 				nb_identity+=1
+			else:
+				if(seq[i] == "-" ):
+					nb_deletion+=1
+				else:
+					if(hsp.hit[i]== "-" ):
+						nb_insertion+=1
 		if (MSA not in data):
 			data[MSA]={}
 
@@ -95,12 +103,16 @@ for file in files_alignement:
 			data[MSA][read_size] = {}
 		match=round(tool_consensus.score_between_two_iupac(hsp.hit.seq,seq.seq),1)
 		error=round(len(seq)-match,1)
+		nb_substitution = round(error - nb_deletion - nb_insertion,1)
 		r_ambiguity=round( (nb_ambiguity/(size_seq)*100) ,1)
 		r_identity=round( (nb_identity/len(seq)*100) ,1)
 		r_match=round( (match/len(seq)*100) ,1)
 		r_error=round( (error/len(seq)*100) ,1)
-		data[MSA][read_size][nb_read]=[nb_ambiguity,r_ambiguity,nb_identity,r_identity,
-		error,r_error,match,r_match,size_seq]
+		r_sub=round((nb_substitution/error*100),1)
+		r_del=round((nb_deletion/error*100),1)
+		r_ins=round((nb_insertion/error*100),1)
+		data[MSA][read_size][nb_read]=[nb_ambiguity,r_ambiguity,nb_identity,r_identity,match,r_match,
+		error,r_error,nb_substitution,r_sub,nb_deletion,r_del,nb_insertion,r_ins,size_seq]
 
 if (TIME == True):
 	pass
@@ -125,7 +137,7 @@ if (TIME == True):
 
 #output
 sep=","
-print("MSA","region_size","depth","number_Ambiguity","percentage_Ambiguity","number_Identity","percentage_Identity","number_Error","percentage_Error","number_Match","percentage_Match","size",sep=sep,end="")
+print("MSA","region_size","depth","number_Ambiguity","percentage_Ambiguity","number_Identity","percentage_Identity","number_Match","percentage_Match","number_Error","percentage_Error","number_Substitution","percentage_Substitution","number_Deletion","percentage_Deletion","number_Insertion","percentage_Insertion","size",sep=sep,end="")
 if (TIME == True):
 	print(sep+"time","elapsed","memory",sep=sep)
 else:

src/tool_consensus.py

@@ -196,7 +196,7 @@ def consensus(alignment,threshold):
 		seq+="-"
 	return seq
 
-#Creation of the consensus sequence
+#Index jaccard for two iupac
 def index_jaccard(nuc_ref,nuc_cons):
 	nb_nuc_ref = len(nuc_ref)
 	nb_nuc_cons = len(nuc_cons)